I suggest you ...

All tagged items could be linked together through semantic relationships such as: "evidence for", "argument against", "relies on", etc. This could potentially culminate in a concept map mode—displaying the web of connections around particular tagged items.

I see you think those suggestions here are hard to execute.
I rather think they are essential for a smart service. I think the more you avoid these, and keep adding hierarchy features to the service, the more you work to make it impossible to ever make that transformation. why do you think this is hard? don't you have the professional manpower on board to go such ways?

What about using something like Glue API / Visual Thesaurus / Thinkmap SDK? visualcomplexity.com showcases 30 semantic web visualisations, including one using delicious tags (http://ivy.fr/revealicious ). Any good for a Diigo development?

What about automated semantic tags? There is so many tag information in the database that it should be no problem to generate a network map of tags from which you would see relations. Is it such a problem to add new relations with a parameter?

What about reducing this idea to link relations, like a "See also"? It would be simpler for users. E.g. one could group an article that is split into separate web pages, or different articles about a specific topic.

@sandy_diigo: it needn't be so complicated... how about enabling the notes feature to work as an interlink between the two nodes (tagged items that need to be semantically related). Like so:
- a 'gmail star'-like functionality can enable us to turn-on a 'note's 'semantic argument' capability
- title of note would become the semantic argument: ex. "evidence for"
- body of note can keep the links of the pointed items, along with their diigo metadata (need not be visually perfect, plain-text is fine)
- pointing mechanism, when 'star' activated' would be the only heavy-coding spot on the GUI side (have guerrilla ideas, but I would rather draw them real-time, if you're interested, than explicate in text)
- after saving such enhanced 'note', it shows up normally in our diigo views; with an added 'semantic connection' see more link, similar to 'show content' or ''+1 annotation" in any results view... better yet, semantic connections could be highlighted by making them similar to the tags' bluish box, only in yellow note color.

I understand that i might be oversimplifying the semantic relationships idea, but for now... with our current technical limitations... I am satisfied with the relationships working as a mental 'note to self' that some external entity (diigo) would classify, and show to me whenever needed